The snapdragon genomes reveal the evolutionary dynamics of theSlocus supergene

AbstractThe multi-allelicS-locus, containing a pistilS-RNaseand dozens ofS-locus F-box (SLF), underlies genetic control of self-incompatibility (SI) inAntirrhinum hispanicum. The genusAntirrhinum, harboring such a SI system has been used as a model to study self-incompatibility extensively. However, there have been limited studies on the genomic organization of theS-locus supergene due to a lack of high-quality genomic data. Here, we present the chromosome-level reference and haplotype-resolved genome assemblies of a self-incompatibleAntirrhinum hispanicumline,AhS7S8. Alongside with the draft genome ofMisopates orontium, comparative genomics reveals thatA.hispanicumdiverged from its self-compatible cousin 12.3 million years ago (Mya). Expanded gene families enriched in distinct functional terms implied different evolutionary trajectories of outcrossing and selfing species. For the first time, two completeA.hispanicum S-haplotypes spanning ∼1.2Mb and containing 32SLFswere reconstructed, while most of theSLFsderived from retroelement-mediated proximal or tandem duplication approximately 122 Mya. Moreover, we detected a candidatecis-transcription factor associated with regulatingSLFs expression, and two miRNAs may control the expression of this transcription factor. Inter-specificS-locus and intra-specificS-haplotype comparisons revealed the dynamic nature and polymorphism of theS-locus supergene mediated by continuous gene duplication, segmental translocation or loss, and TE-involved transposition events. Our data provides an excellent resource for future research on the evolutionary studies onS-RNase-based self-incompatibility system.